Afranche Char is a 19-year-old man who was raised on an island in the Pacific Ocean. The "cell chips" inside his brain contain strange memories and information. Afranche was raised by a man named Gaba Suu, one of the island's elders. On his deathbed, Gaba Suu tells Afranche to go into space, but his lover Everly Key is strongly opposed. One day, a giant humanoid machine washes up on the island's shore, and Afranche makes up his mind to leave.
He soon learns of his history as a literal clone of the legendary Char Aznable and the Zi Zeon organization that created him, And its struggle against the forces of Maha, the Earth Federation government's dreaded "Man-Hunting Agency." Formally known as the 13th Special Investigative Section of the Earth Federation Government Police Agency, this group is responsible for discovering illegal Earth residents and deporting them to the space colonies.
Afranche and his comrades board the Zi Organization's warship "Thirty-One Square." Overruling the ship's captain, renames the Zi Zeon Organization "Metatron" and rechristens the Thirty-One Square as "Mother Metatron."